Contacts of the helix formed by residues 200 - 212 (chain P) in PDB entry 1HH2
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 200 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165P GLU* 4.2 7.6 - - - +
181P TYR* 3.8 28.7 - - + -
183P ILE* 4.8 9.2 - - + -
197P SER* 3.7 20.0 - - - +
199P ARG* 1.3 80.7 - - + +
201P PRO* 1.3 74.7 - - + +
202P GLU* 3.3 16.6 - - + +
203P PHE* 3.1 17.6 + - + +
227P ARG* 3.0 14.3 + - - -
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Residues in contact with PRO 201 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199P ARG 3.8 1.3 - - - +
200P VAL* 1.3 86.6 - - + +
202P GLU* 1.4 72.1 + - - +
204P VAL* 2.9 24.9 + - - +
205P ILE* 3.4 9.3 + - + -
225P ILE* 3.9 27.6 - - + +
227P ARG* 4.1 29.3 - - + +
330P LYS* 6.2 1.8 - - - +
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Residues in contact with GLU 202 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181P TYR* 3.3 50.6 - - + +
200P VAL* 3.3 10.6 - - + +
201P PRO* 1.4 92.3 - - - +
203P PHE* 1.3 59.3 + - - +
205P ILE* 3.6 20.8 - - + +
206P GLY* 2.8 27.4 + - - -
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Residues in contact with PHE 203 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137P VAL* 4.0 5.0 - - + +
167P ILE* 4.4 7.4 - - + -
179P LYS* 3.5 37.9 - - + -
180P VAL* 3.9 3.6 - - - -
181P TYR* 3.8 30.0 - - + -
197P SER 3.9 3.8 - - - -
198P ARG* 3.3 38.6 - - + +
200P VAL* 3.1 20.2 + - + +
201P PRO 3.0 1.2 + - - -
202P GLU* 1.3 77.5 - - - +
204P VAL* 1.3 64.7 + - - +
206P GLY* 3.3 1.9 + - - -
207P LEU* 3.0 45.6 + - + +
227P ARG* 3.9 7.2 - - - +
264P GLU* 3.9 15.3 - - + -
265P LEU* 3.9 16.6 - - + -
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Residues in contact with VAL 204 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201P PRO 2.9 9.4 + - - +
203P PHE* 1.3 79.3 - - - +
205P ILE* 1.3 63.5 + - - +
207P LEU* 3.2 9.2 + - - +
208P MET* 3.0 35.9 + - + +
225P ILE* 3.7 19.7 - - + -
227P ARG* 3.8 36.6 - - - +
233P THR* 4.0 18.8 - - + +
261P ILE* 5.7 1.7 - - + +
265P LEU* 4.2 19.3 - - + -
268P GLU* 4.5 0.2 - - - +
270P LEU* 4.3 13.2 - - + -
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Residues in contact with ILE 205 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201P PRO* 3.4 3.6 + - + +
202P GLU* 3.2 23.8 + - + +
204P VAL* 1.3 77.8 - - - +
206P GLY* 1.3 57.5 + - - +
208P MET* 3.1 7.7 + - - +
209P LYS* 2.9 51.0 + - - +
222P ILE* 3.6 33.9 - - + -
225P ILE* 3.9 34.3 - - + -
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Residues in contact with GLY 206 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136P THR* 5.7 1.6 - - - -
137P VAL* 3.4 28.0 - - - +
181P TYR* 5.4 1.8 - - - -
202P GLU 2.8 12.5 + - - -
205P ILE* 1.3 74.6 - - - +
207P LEU* 1.3 63.7 + - - +
209P LYS* 3.3 13.9 + - - +
210P LEU* 3.0 26.9 + - - +
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Residues in contact with LEU 207 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137P VAL* 4.2 5.8 - - + -
179P LYS* 3.8 26.7 - - + +
203P PHE* 3.0 42.7 + - + +
204P VAL* 3.2 7.8 + - - +
206P GLY* 1.3 75.7 - - - +
208P MET* 1.3 63.3 + - - +
210P LEU* 3.2 7.3 + - + +
211P GLU* 3.0 19.2 + - - +
261P ILE* 3.2 31.8 - - + +
264P GLU* 3.7 35.4 - - + -
265P LEU* 4.0 19.1 - - + -
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Residues in contact with MET 208 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204P VAL* 3.0 30.2 + - + +
205P ILE* 3.3 9.0 - - - +
207P LEU* 1.3 76.8 - - - +
209P LYS* 1.3 54.5 + - - +
211P GLU 3.3 0.2 + - - -
212P ILE* 2.8 54.0 + - + +
215P VAL* 4.1 4.7 - - + -
222P ILE* 3.9 29.6 - - + -
225P ILE* 5.4 0.2 - - - -
235P VAL* 3.9 34.3 - - + -
237P VAL* 4.1 7.6 - - + -
250P CYS* 4.1 27.6 - - + -
261P ILE* 4.2 11.9 - - + -
270P LEU* 5.0 8.5 - - + -
272P VAL* 5.1 3.4 - - + -
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Residues in contact with LYS 209 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135P GLY 5.5 4.7 - - - -
205P ILE* 2.9 36.9 + - - +
206P GLY* 3.3 13.4 + - - +
208P MET* 1.3 76.0 - - - +
210P LEU* 1.3 63.1 + - + +
212P ILE 3.7 6.2 + - - +
213P PRO* 5.1 0.3 - - - +
215P VAL* 3.8 30.5 + - + +
216P GLU* 3.0 45.5 + - - +
222P ILE* 5.6 0.6 - - - +
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Residues in contact with LEU 210 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137P VAL* 3.8 37.2 - - + +
138P THR* 5.6 0.2 - - - -
179P LYS* 3.0 34.1 - - + +
206P GLY 3.0 13.5 + - - +
207P LEU* 3.5 11.2 - - + +
208P MET 3.1 0.4 - - - -
209P LYS* 1.3 80.0 - - + +
211P GLU* 1.3 71.4 + - + +
212P ILE 3.9 0.2 + - - -
213P PRO* 5.5 1.0 - - - +
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Residues in contact with GLU 211 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179P LYS* 5.3 5.4 + - - -
207P LEU 3.0 4.6 + - - +
208P MET 4.4 0.4 - - - +
210P LEU* 1.3 87.3 - - - +
212P ILE* 1.3 60.6 - - + +
213P PRO* 3.5 7.6 - - - +
257P ARG* 3.4 41.2 + - + +
260P ALA* 3.2 38.0 - - + +
261P ILE* 3.5 25.7 - - + +
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Residues in contact with ILE 212 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208P MET* 2.8 36.0 + - + +
209P LYS 3.7 4.9 - - - +
210P LEU 3.5 1.0 - - - -
211P GLU* 1.3 87.4 - - + +
213P PRO* 1.3 68.6 - - - +
214P GLU* 3.8 13.5 - - + +
215P VAL* 2.9 37.2 + - + +
216P GLU 3.2 7.8 + - - -
220P VAL* 5.3 0.4 - - + -
249P ALA* 3.6 22.0 - - + +
250P CYS* 3.4 45.5 - - + +
257P ARG* 4.5 2.5 - - + +
261P ILE* 5.5 4.9 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il